use Bio::Matrix::PSM::InstanceSite;
#You can get an InstanceSite object either from a file:
my ($instances,$matrix)=$SomePSMFile->parse_next;
#or from memory
my %params=(seq=>'TATAAT',
id=>"TATAbox1", accession=>'ENSG00000122304', mid=>'TB1',
desc=>'TATA box, experimentally verified in PRM1 gene',
-relpos=>-35, -anchor=>'CHR7', -start=>35000921, -end=>35000926);
#Last 2 arguments are passed to create a Bio::LocatableSeq object
#Anchor shows the coordinates system for the Bio::LocatableSeq object

Description

Abstract interface to PSM site occurrence (PSM sequencematch). InstanceSite objects may be used to describe a PSM (SeeBio::Matrix::PSM::SiteMatrix) sequence matches. The usualcharacteristic of such a match is sequence coordinates, score,sequence and sequence (gene) identifier- accession number or other id.This object inherits from Bio::LocatableSeq (which defines the realsequence) and might hold a SiteMatrix object, used to detect the CRE(cis-regulatory element), or created from this CRE.While the documentation states that the motif id and gene id(accession) combination should be unique, this is not entirely true-there might be more than one occurrence of the same cis-regulatoryelement in the upstream region of the same gene. Therefore relposwould be the third element to create a really unique combination.

Title : relpos Usage : my $seqpos=$instance->relpos; Function: Get/Set the relative position of the instance with respect to the transcription start site (if known). Can and usually is negative. Throws : Example : Returns : integer Args : integer

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